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    R3HDM1 R3H domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23518, updated on 3-Nov-2024

    Summary

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    Official Symbol
    R3HDM1provided by HGNC
    Official Full Name
    R3H domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:9757
    See related
    Ensembl:ENSG00000048991 MIM:619474; AllianceGenome:HGNC:9757
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    R3HDM
    Summary
    Enables RNA binding activity. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 20.1), testis (RPKM 10.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See R3HDM1 in Genome Data Viewer
    Location:
    2q21.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135531484..135725269)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (135972007..136165780)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (136289054..136482839)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906077 Neighboring gene zinc finger RANBP2-type containing 3 Neighboring gene MPRA-validated peak3875 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16572 Neighboring gene Sharpr-MPRA regulatory region 5980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11981 Neighboring gene G3BP1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16574 Neighboring gene uncharacterized LOC124907893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16575 Neighboring gene RNA, U6 small nuclear 512, pseudogene Neighboring gene microRNA 128-1 Neighboring gene uncharacterized LOC107985946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16577 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136499891-136500666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:136554979-136555500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136555501-136556024 Neighboring gene UBX domain protein 4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:136574960-136576159 Neighboring gene LCT antisense RNA 1 Neighboring gene lactase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. R3HDM1 haploinsufficiency is associated with mild intellectual disability. Fukushi D, et al. Am J Med Genet A, 2021 Jun. PMID 33750005
    2. Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. Ficarro SB, et al. Rapid Commun Mass Spectrom, 2005. PMID 15570572
    3. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1 (supplement). Nomura N, et al. DNA Res, 1994. PMID 7584028
    4. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. Nomura N, et al. DNA Res, 1994. PMID 7584026
    5. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. Brill LM, et al. Anal Chem, 2004 May 15. PMID 15144186

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. R3HDM1 haploinsufficiency is associated with mild intellectual disability.
      Title: R3HDM1 haploinsufficiency is associated with mild intellectual disability.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of R3H domain containing 1 (R3HDM1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23334, KIAA0029

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    R3H domain-containing protein 1
    Names
    R3H domain (binds single-stranded nucleic acids) containing

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001282798.2 → NP_001269727.1  R3H domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_001269727.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC011893, AC016742, AK290015, BQ011745, D21852, DA324823
      Consensus CDS
      CCDS63025.1
      UniProtKB/Swiss-Prot
      Q15032
      Related
      ENSP00000387010.1, ENST00000409606.5
      Conserved Domains (3) summary
      cd02642
      Location:167 → 228
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam09606
      Location:579 → 910
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam12752
      Location:251 → 302
      SUZ; SUZ domain

    2. NM_001282799.2 → NP_001269728.1  R3H domain-containing protein 1 isoform c

      See identical proteins and their annotated locations for NP_001269728.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks two alternate exons that result in the loss of an in-frame segment in the 5' coding region, and lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC016742, AL704414, BQ011745, D21852
      Consensus CDS
      CCDS63026.1
      UniProtKB/TrEMBL
      B4DLH6
      Related
      ENSP00000386457.1, ENST00000409478.5
      Conserved Domains (2) summary
      cd02642
      Location:123 → 184
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam12752
      Location:205 → 258
      SUZ; SUZ domain

    3. NM_001282800.2 → NP_001269729.1  R3H domain-containing protein 1 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AC016742, AK127793, BQ011745
      Consensus CDS
      CCDS63024.1
      UniProtKB/Swiss-Prot
      Q15032
      Related
      ENSP00000386877.1, ENST00000410054.5
      Conserved Domains (2) summary
      cd02642
      Location:111 → 172
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam12752
      Location:193 → 246
      SUZ; SUZ domain

    4. NM_001354199.2 → NP_001341128.1  R3H domain-containing protein 1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC011893, AC016742, BQ011745
      Consensus CDS
      CCDS2177.1
      UniProtKB/Swiss-Prot
      A8K1V0, B3KXQ9, E9PBB4, E9PG42, G5E9G8, Q15032, Q8IW32
      Conserved Domains (3) summary
      cd02642
      Location:167 → 228
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam09606
      Location:578 → 909
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam12752
      Location:251 → 302
      SUZ; SUZ domain

    5. NM_001354200.2 → NP_001341129.1  R3H domain-containing protein 1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Both variants 1 and 6 encoded the same isoform (a).
      Source sequence(s)
      AC011893, AC016742, BQ011745
      Consensus CDS
      CCDS63025.1
      Conserved Domains (3) summary
      cd02642
      Location:167 → 228
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam09606
      Location:579 → 910
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam12752
      Location:251 → 302
      SUZ; SUZ domain

    6. NM_001378107.1 → NP_001365036.1  R3H domain-containing protein 1 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC011893, AC016742
      Consensus CDS
      CCDS92870.1
      UniProtKB/TrEMBL
      A0A804HIA8
      Related
      ENSP00000506980.1, ENST00000683871.1
      Conserved Domains (3) summary
      cd02642
      Location:167 → 228
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam03157
      Location:653 → 855
      Glutenin_hmw; High molecular weight glutenin subunit
      pfam12752
      Location:251 → 302
      SUZ; SUZ domain

    7. NM_015361.4 → NP_056176.2  R3H domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_056176.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (b) is 1 aa shorter than isoform a.
      Source sequence(s)
      AK026987, AL704414, BC041093, BQ011745
      Consensus CDS
      CCDS2177.1
      UniProtKB/Swiss-Prot
      A8K1V0, B3KXQ9, E9PBB4, E9PG42, G5E9G8, Q15032, Q8IW32
      Related
      ENSP00000264160.4, ENST00000264160.8
      Conserved Domains (3) summary
      cd02642
      Location:167 → 228
      R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
      pfam09606
      Location:578 → 909
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam12752
      Location:251 → 302
      SUZ; SUZ domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      135531484..135725269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      135972007..136165780
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15032.3 GenPept UniProtKB/Swiss-Prot:Q15032

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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